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Nicolè S, Barcaccia G, Erickson DL, Kress JW, Lucchin M. The coding region of the UFGT gene is a source of diagnostic SNP markers that allow single-locus DNA genotyping for the assessment of cultivar identity and ancestry in grapevine (Vitis vinifera L.). BMC Res Notes 2013; 6:502. [PMID: 24298902 PMCID: PMC4222114 DOI: 10.1186/1756-0500-6-502] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 11/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vitis vinifera L. is one of society's most important agricultural crops with a broad genetic variability. The difficulty in recognizing grapevine genotypes based on ampelographic traits and secondary metabolites prompted the development of molecular markers suitable for achieving variety genetic identification. FINDINGS Here, we propose a comparison between a multi-locus barcoding approach based on six chloroplast markers and a single-copy nuclear gene sequencing method using five coding regions combined with a character-based system with the aim of reconstructing cultivar-specific haplotypes and genotypes to be exploited for the molecular characterization of 157 V. vinifera accessions. The analysis of the chloroplast target regions proved the inadequacy of the DNA barcoding approach at the subspecies level, and hence further DNA genotyping analyses were targeted on the sequences of five nuclear single-copy genes amplified across all of the accessions. The sequencing of the coding region of the UFGT nuclear gene (UDP-glucose: flavonoid 3-0-glucosyltransferase, the key enzyme for the accumulation of anthocyanins in berry skins) enabled the discovery of discriminant SNPs (1/34 bp) and the reconstruction of 130 V. vinifera distinct genotypes. Most of the genotypes proved to be cultivar-specific, and only few genotypes were shared by more, although strictly related, cultivars. CONCLUSION On the whole, this technique was successful for inferring SNP-based genotypes of grapevine accessions suitable for assessing the genetic identity and ancestry of international cultivars and also useful for corroborating some hypotheses regarding the origin of local varieties, suggesting several issues of misidentification (synonymy/homonymy).
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Affiliation(s)
- Silvia Nicolè
- Laboratory of Plant Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis - Viale Università 16, 35020 Padova, Legnaro, Italy
| | - Gianni Barcaccia
- Laboratory of Plant Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis - Viale Università 16, 35020 Padova, Legnaro, Italy
| | - David L Erickson
- Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012 USA
| | - John W Kress
- Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012 USA
| | - Margherita Lucchin
- Laboratory of Plant Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis - Viale Università 16, 35020 Padova, Legnaro, Italy
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Bouby L, Figueiral I, Bouchette A, Rovira N, Ivorra S, Lacombe T, Pastor T, Picq S, Marinval P, Terral JF. Bioarchaeological insights into the process of domestication of grapevine (Vitis vinifera L.) during Roman times in Southern France. PLoS One 2013; 8:e63195. [PMID: 23690998 PMCID: PMC3654964 DOI: 10.1371/journal.pone.0063195] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/28/2013] [Indexed: 12/01/2022] Open
Abstract
Grapevine (Vitis vinifera), one of the most important fruit species in the Classical Mediterranean world, is thought to have been domesticated first in South-Western Asia, during the Neolithic. However, the domestication process remains largely unknown. Crucial unanswered questions concern the duration of the process (rapid or slow?) and the related geographical area (single or multiple-origins?). Seeds from domesticated grapevine and from its wild ancestor are reported to differ according to shape. Our work aims, first, to confirm this difference and secondly to identify the extent of domestication in the grapes cultivated by Romans in Southern France during the period 50 BCE–500 CE. We had the opportunity to analyze uncharred waterlogged grape pips from 17 archaeological sites. Based on an extended reference sample of modern wild grapevines and cultivars our work shows that both subspecies can be discriminated using simple measurements. The elongation gradient of the pip’s body and stalk may be regarded as an indicator of the strength of the selection pressures undergone by domesticated grapes. Grapevines cultivated during the Roman period included a mix of morphotypes comprising wild, intermediate and moderately selected domesticated forms. Our data point to a relative shift towards more selected types during the Roman period. Domestication of the grapevine appears to have been a slow process. This could result from the recurrent incorporation into cultivation of plants originating from sexual reproduction, when grape cultivation essentially relies on vegetative propagation.
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Affiliation(s)
- Laurent Bouby
- CNRS, Centre de Bio-Archéologie et d'Ecologie (CBAE), UMR 5059, Montpellier, France.
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Emanuelli F, Lorenzi S, Grzeskowiak L, Catalano V, Stefanini M, Troggio M, Myles S, Martinez-Zapater JM, Zyprian E, Moreira FM, Grando MS. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape. BMC PLANT BIOLOGY 2013; 13:39. [PMID: 23497049 PMCID: PMC3610244 DOI: 10.1186/1471-2229-13-39] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 02/27/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples. RESULTS We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability. CONCLUSIONS The comprehensive molecular characterization of our grape germplasm collection contributes to the knowledge about levels and distribution of genetic diversity in the existing resources of Vitis and provides insights into genetic subdivision within the European germplasm. Genotypic and phenotypic information compared in this study may efficiently guide further exploration of this diversity for facilitating its practical use.
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Affiliation(s)
- Francesco Emanuelli
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Silvia Lorenzi
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Lukasz Grzeskowiak
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Valentina Catalano
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Marco Stefanini
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Michela Troggio
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, B2N 5E3, Canada
| | - José M Martinez-Zapater
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), C/ Madre de dios 51, Logroño, 26006, Spain
| | - Eva Zyprian
- JKI Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, 76833, Germany
| | - Flavia M Moreira
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
- Instituto Federal de Santa Catarina, Rua José Lino Kretzer 608 - Praia Comprida, São José, Santa Catarina, 88130-310, Brasil
| | - M Stella Grando
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
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Bacilieri R, Lacombe T, Le Cunff L, Di Vecchi-Staraz M, Laucou V, Genna B, Péros JP, This P, Boursiquot JM. Genetic structure in cultivated grapevines is linked to geography and human selection. BMC PLANT BIOLOGY 2013; 13:25. [PMID: 23394135 PMCID: PMC3598926 DOI: 10.1186/1471-2229-13-25] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 01/31/2013] [Indexed: 05/19/2023]
Abstract
BACKGROUND Grapevine (Vitis vinifera subsp. vinifera) is one of the most important and ancient horticultural plants in the world. Domesticated about 8-10,000 years ago in the Eurasian region, grapevine evolved from its wild relative (V. vinifera subsp. sylvestris) into very diverse and heterozygous cultivated forms. In this work we study grapevine genetic structure in a large sample of cultivated varieties, to interpret the wide diversity at morphological and molecular levels and link it to cultivars utilization, putative geographic origin and historical events. RESULTS We analyzed the genetic structure of cultivated grapevine using a dataset of 2,096 multi-locus genotypes defined by 20 microsatellite markers. We used the Bayesian approach implemented in the STRUCTURE program and a hierarchical clustering procedure based on Ward's method to assign individuals to sub-groups. The analysis revealed three main genetic groups defined by human use and geographic origin: a) wine cultivars from western regions, b) wine cultivars from the Balkans and East Europe, and c) a group mainly composed of table grape cultivars from Eastern Mediterranean, Caucasus, Middle and Far East countries. A second structure level revealed two additional groups, a geographic group from the Iberian Peninsula and Maghreb, and a group comprising table grapes of recent origins from Italy and Central Europe. A large number of admixed genotypes were also identified. Structure clusters regrouped together a large proportion of family-related genotypes. In addition, Ward's method revealed a third level of structure, corresponding either to limited geographic areas, to particular grape use or to family groups created through artificial selection and breeding. CONCLUSIONS This study provides evidence that the cultivated compartment of Vitis vinifera L. is genetically structured. Genetic relatedness of cultivars has been shaped mostly by human uses, in combination with a geographical effect. The finding of a large portion of admixed genotypes may be the trace of both large human-mediated exchanges between grape-growing regions throughout history and recent breeding.
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Affiliation(s)
- Roberto Bacilieri
- Institut National de la Recherche Agronomique, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
| | - Thierry Lacombe
- Institut National de la Recherche Agronomique, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
- INRA - Domaine de Vassal. Ancienne route de Sète, 34340, Marseillan Plage, France
| | - Loïc Le Cunff
- Institut Français de la Vigne et du Vin - Unité Mixte Technologique Géno-Vigne, 2 Place P. Viala, 34060, Montpellier, France
| | - Manuel Di Vecchi-Staraz
- Institut National de la Recherche Agronomique, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
| | - Valérie Laucou
- Institut National de la Recherche Agronomique, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
| | - Blaise Genna
- INRA - Domaine de Vassal. Ancienne route de Sète, 34340, Marseillan Plage, France
| | - Jean-Pierre Péros
- Institut National de la Recherche Agronomique, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
| | - Patrice This
- Institut National de la Recherche Agronomique, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
| | - Jean-Michel Boursiquot
- Montpellier SupAgro, UMR 1334 AGAP Amélioration génétique et adaptation de plantes, équipe DAVEM, 2 Place P. Viala, 34060, Montpellier, France
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55
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Goto-Yamamoto N, Azuma A, Mitani N, Kobayashi S. SSR Genotyping of Wild Grape Species and Grape Cultivars of Vitis vinifera and V. vinifera ^|^times; V. labrusca. ACTA ACUST UNITED AC 2013. [DOI: 10.2503/jjshs1.82.125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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56
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Computer vision as a method complementary to molecular analysis: Grapevine cultivar seeds case study. C R Biol 2012; 335:602-15. [DOI: 10.1016/j.crvi.2012.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/07/2012] [Accepted: 08/07/2012] [Indexed: 11/13/2022]
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De Andrés MT, Benito A, Pérez-Rivera G, Ocete R, Lopez MA, Gaforio L, Muñoz G, Cabello F, Martínez Zapater JM, Arroyo-García R. Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines. Mol Ecol 2011; 21:800-16. [PMID: 22151598 DOI: 10.1111/j.1365-294x.2011.05395.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The wild grapevine, Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain, natural populations of V. vinifera ssp. sylvestris can still be found along river banks. In this work, we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analysed the possible coexistence in the natural habitat of wild grapevines with naturalized grapevine cultivars and rootstocks. In this way, phenotypic and genetic analyses identified 19% of the collected samples as derived from cultivated genotypes, being either naturalized cultivars or hybrid genotypes derived from spontaneous crosses between wild and cultivated grapevines. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated germplasm and wild germplasm are genetically divergent with low level of introgression. Using a model-based approach implemented in the software structure, we identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships between wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current Western cultivars.
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Affiliation(s)
- M T De Andrés
- Departamento de Investigación Agroalimentaria, IMIDRA, Finca El Encín, Apto 127, 28800 Alcalá de Henares, Madrid, Spain
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58
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Laucou V, Lacombe T, Dechesne F, Siret R, Bruno JP, Dessup M, Dessup T, Ortigosa P, Parra P, Roux C, Santoni S, Varès D, Péros JP, Boursiquot JM, This P. High throughput analysis of grape genetic diversity as a tool for germplasm collection management. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1233-45. [PMID: 21234742 DOI: 10.1007/s00122-010-1527-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 12/22/2010] [Indexed: 05/20/2023]
Abstract
Using 20 SSR markers well scattered across the 19 grape chromosomes, we analyzed 4,370 accessions of the INRA grape repository at Vassal, mostly cultivars of Vitis vinifera subsp. sativa (3,727), but also accessions of V. vinifera subsp. sylvestris (80), interspecific hybrids (364), and rootstocks (199). The analysis revealed 2,836 SSR single profiles: 2,323 sativa cultivars, 72 wild individuals (sylvestris), 306 interspecific hybrids, and 135 rootstocks, corresponding to 2,739 different cultivars in all. A total of 524 alleles were detected, with a mean of 26.20 alleles per locus. For the 2,323 cultivars of V. vinifera, 338 alleles were detected with a mean of 16.9 alleles per locus. The mean genetic diversity (GDI) was 0.797 and the level of heterozygosity was 0.76, with broad variation from 0.20 to 1. Interspecific hybrids and rootstocks were more heterozygous and more diverse (GDI = 0.839 and 0.865, respectively) than V. vinifera cultivars (GDI = 0.769), Vitis vinifera subsp. sylvestris being the least divergent with GDI = 0.708. Principal coordinates analysis distinguished the four groups. Slight clonal polymorphism was detected. The limit between clonal variation and cultivar polymorphism was set at four allelic differences out of 40. SSR markers were useful as a complementary tool to traditional ampelography for cultivar identification. Finally, a set of nine SSR markers was defined that was sufficient to distinguish 99.8% of the analyzed accessions. This set is suitable for routine characterization and will be valuable for germplasm management.
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Affiliation(s)
- V Laucou
- INRA Montpellier SupAgro, UMR DIAPC, Equipe Génétique de la Vigne, Montpellier, France.
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Myles S, Boyko AR, Owens CL, Brown PJ, Grassi F, Aradhya MK, Prins B, Reynolds A, Chia JM, Ware D, Bustamante CD, Buckler ES. Genetic structure and domestication history of the grape. Proc Natl Acad Sci U S A 2011; 108:3530-5. [PMID: 21245334 PMCID: PMC3048109 DOI: 10.1073/pnas.1009363108] [Citation(s) in RCA: 321] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. sylvestris from the US Department of Agriculture grape germplasm collection. We find support for a Near East origin of vinifera and present evidence of introgression from local sylvestris as the grape moved into Europe. High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera, which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. The considerable genetic diversity within vinifera, however, is contained within a complex network of close pedigree relationships that has been generated by crosses among elite cultivars. We show that first-degree relationships are rare between wine and table grapes and among grapes from geographically distant regions. Our results suggest that although substantial genetic diversity has been maintained in the grape subsequent to domestication, there has been a limited exploration of this diversity. We propose that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity.
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Affiliation(s)
- Sean Myles
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Department of Biology, Acadia University, Wolfville, NS, Canada B4P 2R6
- Department of Plant and Animal Sciences, Nova Scotia Agricultural College, Truro, NS, Canada B2N 5E3
| | - Adam R. Boyko
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Christopher L. Owens
- Grape Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Cornell University, Geneva, NY 14456
| | - Patrick J. Brown
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | - Fabrizio Grassi
- Botanical Garden, Department of Biology, University of Milan, 20133 Milan, Italy
| | - Mallikarjuna K. Aradhya
- National Clonal Germplasm Repository, United States Department of Agriculture-Agricultural Research Service, University of California, Davis, CA 95616
| | - Bernard Prins
- National Clonal Germplasm Repository, United States Department of Agriculture-Agricultural Research Service, University of California, Davis, CA 95616
| | - Andy Reynolds
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Jer-Ming Chia
- Cold Spring Harbor Laboratory, United States Department of Agriculture-Agricultural Research Service, Cold Spring Harbor, NY 11724; and
| | - Doreen Ware
- Cold Spring Harbor Laboratory, United States Department of Agriculture-Agricultural Research Service, Cold Spring Harbor, NY 11724; and
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Cornell University, Ithaca, NY14853
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Cornell University, Ithaca, NY14853
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Zecca G, De Mattia F, Lovicu G, Labra M, Sala F, Grassi F. Wild grapevine: silvestris, hybrids or cultivars that escaped from vineyards? Molecular evidence in Sardinia. PLANT BIOLOGY (STUTTGART, GERMANY) 2010; 12:558-62. [PMID: 20522194 DOI: 10.1111/j.1438-8677.2009.00226.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Vitis vinifera ssp. silvestris, the spontaneous subspecies of V. vinifera L., is believed to be the ancestor of present grapevine cultivars. In this work, polymorphism at 13 SSR loci was investigated to answer the following key question: are wild plants (i) true silvestris, (ii) hybrids between wild and cultivated plants or (iii) or 'escapes' from vineyards? In particular, the objective of the present study was to identify truly wild individuals and to search for possible hybridization events. The study was performed in Sardinia, the second largest island in the Mediterranean Sea, which is characterized by a large and well-described number of both grape cultivars and wild populations. This region was ideal for the study because of its spatial isolation and, consequently, limited contamination from outside material. The results of this study show that domesticated and wild grapevine germplasms are genetically divergent and thus are real silvestris. Pure lineages (both domesticated and wild) show very high average posterior probabilities of assignment to their own clusters, with a low level of introgression.
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Affiliation(s)
- G Zecca
- Botanical Garden, Department of Biology, University of Milan, Milano, Italy.
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61
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Lopes MS, Mendonça D, Rodrigues dos Santos M, Eiras-Dias JE, da Câmara Machado A. New insights on the genetic basis of Portuguese grapevine and on grapevine domestication. Genome 2010; 52:790-800. [PMID: 19935927 DOI: 10.1139/g09-048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As the ancestor of cultivated grape, Vitis vinifera subsp. sylvestris represents a unique, invaluable genetic resource for the improvement of cultivated grapevines. Recently, five populations of wild grapevines were identified in Portugal. Sixty vines were characterized with 11 nuclear SSR markers and further compared with 70 genotypes of Portuguese Vitis vinifera subsp. sativa. The obtained data demonstrate moderate genetic differentiation between wild grapevine populations and moderate to high genetic differentiation between wild and cultivated grapevines. However, the identification of high degrees of similarity between wild and cultivated grapes (up to 87%) and a putative parent-progeny relationship between wild and cultivated grapes with 17 additional SSR markers is indicative of gene flow between local wild grapevine populations and Portuguese domesticated vines. Also, the ancestry of some Azorean cultivars was ascertained. The obtained data further support the hypothesis of several domestication centres, with Portugal, Spain, and Italy playing a particular role after the last glaciation, giving rise to many of the Western European cultivars.
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Affiliation(s)
- M S Lopes
- Centro de Biotecnologia dos Açores, Departamento de Ciências Agrárias, Universidade dos Açores, Terra-Chã, 9701-851 Angra do Heroísmo, Portugal
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62
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Terral JF, Tabard E, Bouby L, Ivorra S, Pastor T, Figueiral I, Picq S, Chevance JB, Jung C, Fabre L, Tardy C, Compan M, Bacilieri R, Lacombe T, This P. Evolution and history of grapevine (Vitis vinifera) under domestication: new morphometric perspectives to understand seed domestication syndrome and reveal origins of ancient European cultivars. ANNALS OF BOTANY 2010; 105:443-55. [PMID: 20034966 PMCID: PMC2826248 DOI: 10.1093/aob/mcp298] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 10/05/2009] [Accepted: 11/03/2009] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS In spite of the abundance of archaeological, bio-archaeological, historical and genetic data, the origins, historical biogeography, identity of ancient grapevine cultivars and mechanisms of domestication are still largely unknown. Here, analysis of variation in seed morphology aims to provide accurate criteria for the discrimination between wild grapes and modern cultivars and to understand changes in functional traits in relation to the domestication process. This approach is also used to quantify the phenotypic diversity in the wild and cultivated compartments and to provide a starting point for comparing well-preserved archaeological material, in order to elucidate the history of grapevine varieties. METHODS Geometrical analysis (elliptic Fourier transform method) was applied to grapevine seed outlines from modern wild individuals, cultivars and well-preserved archaeological material from southern France, dating back to the first to second centuries. KEY RESULTS AND CONCLUSIONS Significant relationships between seed shape and taxonomic status, geographical origin (country or region) of accessions and parentage of varieties are highlighted, as previously noted based on genetic approaches. The combination of the analysis of modern reference material and well-preserved archaeological seeds provides original data about the history of ancient cultivated forms, some of them morphologically close to the current 'Clairette' and 'Mondeuse blanche' cultivars. Archaeobiological records seem to confirm the complexity of human contact, exchanges and migrations which spread grapevine cultivation in Europe and in Mediterranean areas, and argue in favour of the existence of local domestication in the Languedoc (southern France) region during Antiquity.
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Affiliation(s)
- Jean-Frédéric Terral
- Centre de Bio-Archéologie et d'Ecologie, Equipe Ressources Biologiques, Sociétés, Biodiversité-UMR 5059 CNRS/UM2/EPHE, Institut de Botanique (Université Montpellier 2), 163 Rue Auguste Broussonet, 34090 Montpellier, France.
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63
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Jánváry L, Hoffmann T, Pfeiffer J, Hausmann L, Töpfer R, Fischer TC, Schwab W. A double mutation in the anthocyanin 5-O-glucosyltransferase gene disrupts enzymatic activity in Vitis vinifera L. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2009; 57:3512-3518. [PMID: 19338353 DOI: 10.1021/jf900146a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The inability of most European grapevines ( Vitis vinifera ) to produce 3,5-di-O-glucosides of anthocyanidin-3-O-glucosides while in other Vitis species diglucosides are found has long been used as a diagnostic tool for the classification of wines according to their varietal origin. A functional 5-O-glucosyltransferase (5GT) gene and its nonfunctional allele were recently cloned from the heterozygous hybrid cultivar 'Regent'. Protein sequence comparison revealed only five amino acid substitutions and a truncation at the C-terminus in the inactive enzyme. Restoration of the C-terminus in the European allele alone proved to be insufficient for a reversal to a functional allele. An additional V121L transition located in close spatial vicinity of the catalytically active histidine in the active site of the nonfunctional protein was also essential to recover 5GT activity. Thus, two mutations render the 5GT inactive in V. vinifera and explain why revertants for this mutant allele have not been observed in breeding programs. The results have a significant effect on the classification and breeding of Vitis varieties and the evaluation of derived products.
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Affiliation(s)
- László Jánváry
- Biomolecular Food Technology, Technische Universität München, Hochfeldweg 1, 85354 Freising, Germany
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64
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Salmaso M, Valle RD, Lucchin M. Gene pool variation and phylogenetic relationships of an indigenous northeast Italian grapevine collection revealed by nuclear and chloroplast SSRs. Genome 2009; 51:838-55. [PMID: 18923535 DOI: 10.1139/g08-064] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A germplasm safeguard programme was set up with 19 grapevine varieties considered as indigenous to northeastern Italy. To better estimate how genetic structure can be used to obtain a conservation perspective of local varieties, genetic variability was examined at 30 nuclear and 3 chloroplast polymorphic microsatellite loci in the native varieties plus 7 European cultivars taken as reference. The genetic profiles of all the cultivars were searched for possible parentage relationships and several suspected cases of the same variety having different names were investigated. The alleles shared at the loci suggest a parent-offspring relationship between Merlot and Cabernet Franc, 'Gruaja' and 'Negrara Veronese', and Marzemina Nera and Marzemina Bianca. Alleles at the 30 nuclear loci are consistent with Raboso Veronese being the progeny of Marzemina Bianca and Raboso Piave. Chloroplast-specific haplotypes were singled out for the first time in this indigenous germplasm and should be considered typical of the region. It is hypothesized that there are many specific haplotypes for the local varieties due to a past contribution of wild grapevine to the cultivated gene pool. The majority of investigated cultivars were demonstrated to constitute an independent source of genetic variation, and therefore a possible valuable resource of genetic traits for breeders.
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Affiliation(s)
- Marzia Salmaso
- Department of Environmental Agronomy and Crop Production, Agripolis, University of Padova, Viale Universita 16, 35020 Legnaro, Padova, Italy.
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65
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GRASSI FABRIZIO, DE MATTIA FABRIZIO, ZECCA GIOVANNI, SALA FRANCESCO, LABRA MASSIMO. Historical isolation and Quaternary range expansion of divergent lineages in wild grapevine. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01081.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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66
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Di Vecchi-Staraz M, Laucou V, Bruno G, Lacombe T, Gerber S, Bourse T, Boselli M, This P. Low level of pollen-mediated gene flow from cultivated to wild grapevine: consequences for the evolution of the endangered subspecies Vitis vinifera L. subsp. silvestris. ACTA ACUST UNITED AC 2008; 100:66-75. [PMID: 18927474 DOI: 10.1093/jhered/esn084] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
A parentage and a paternity-based approach were tested for estimation of pollen-mediated gene flow in wild grapevine (Vitis vinifera L. subsp. silvestris), a wind-pollinated species occurring in Mediterranean Europe and southwestern Asia. For this purpose, 305 seedlings collected in 2 years at 2 locations in France from 4 wild female individuals and 417 wild individuals prospected from France and Italy were analyzed using 20 highly polymorphic microsatellite loci. Their profiles were compared with a database consisting of 3203 accessions from the Institut National de la Recherche Agronomique Vassal collection including cultivars, rootstocks, interspecific hybrids, and other wild individuals. Paternity was assigned for 202 (66.2%) of the 305 seedlings, confirming the feasibility of the method. Most of the fertilizing pollen could be assigned to wild males growing nearby. Estimates of pollen immigration from the cultivated compartment (i.e., the totality of cultivars) ranged from 4.2% to 26% from nearby vineyards and from hidden pollinators such as cultivars and rootstocks that had escaped from farms. In an open landscape, the pollen flow was correlated to the distance between individuals, the main pollinator being the closest wild male (accounting for 51.4-86.2% of the pollen flow). In a closed landscape, more complex pollination occurred. Analysis of the parentage of the 417 wild individuals also revealed relationships between nearby wild individuals, but in the case of 12 individuals (3%), analysis revealed pollen immigration from vineyards, confirming the fitness of the hybrid seedlings. These pollen fluxes may have a significant effect on the evolution of wild populations: on the one hand, the low level of pollen-mediated gene flow from cultivated to wild grapevine could contribute to a risk of extinction of the wild compartment (i.e., the totality of the wild individuals). On the other hand, pollen dispersal within the wild populations may induce inbreeding depression of wild grapevines.
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Affiliation(s)
- Manuel Di Vecchi-Staraz
- Institut National de la Recherche Agronomique, UMR 1097, Diversité et Adaptation des plantes Equipe Diversité, Génétique et génomique Vigne, 2, Place Viala, 34060 Montpellier, France
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67
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Study of genetic relationships between wild and domesticated grapevine distributed from Middle East Regions to European countries. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s12210-008-0016-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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68
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Arrigo N, Arnold C. Naturalised Vitis rootstocks in Europe and consequences to native wild grapevine. PLoS One 2007; 2:e521. [PMID: 17565374 PMCID: PMC1885978 DOI: 10.1371/journal.pone.0000521] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2006] [Accepted: 05/15/2007] [Indexed: 11/24/2022] Open
Abstract
The genus Vitis is represented by several coexisting species in Europe. Our study focuses on naturalised rootstocks that originate in viticulture. The consequences of their presence to the landscape and to native European species (Vitis vinifera ssp. silvestris) are evaluated. This study compares ecological traits (seven qualitative and quantitative descriptors) and the genetic diversity (10 SSR markers) of populations of naturalised rootstocks and native wild grapevines. 18 large naturalised rootstock populations were studied in the Rhône watershed. Wild European grapevines are present in four main habitats (screes, alluvial forests, hedges, and streamside hedges). In contrast, naturalised rootstock populations are mainly located in alluvial forests, but they clearly take advantage of alluvial system dynamics and connectivity at the landscape level. These latter populations appear to reproduce sexually, and show a higher genetic diversity than Vitis vinifera ssp. silvestris. The regrouping of naturalised rootstocks in interconnected populations tends to create active hybrid swarms of rootstocks. The rootstocks show characters of invasive plants. The spread of naturalised rootstocks in the environment, the acceleration of the decline of the European wild grapevine, and the propagation of genes of viticultural interest in natural populations are potential consequences that should be kept in mind when undertaking appropriate management measures.
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Affiliation(s)
- Nils Arrigo
- Laboratory of Evolutionary Botany, University of Neuchâtel, Neuchâtel, Switzerland
| | - Claire Arnold
- National Centre of Competence in Research (NCCR) Plant Survival, University of Neuchâtel, Neuchâtel, Switzerland
- * To whom correspondence should be addressed. E-mail:
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69
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Sarri V, Baldoni L, Porceddu A, Cultrera NGM, Contento A, Frediani M, Belaj A, Trujillo I, Cionini PG. Microsatellite markers are powerful tools for discriminating among olive cultivars and assigning them to geographically defined populations. Genome 2007; 49:1606-15. [PMID: 17426775 DOI: 10.1139/g06-126] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Twelve simple sequence repeat (SSR) loci were used to differentiate among 118 cultivars sampled in several countries of the Mediterranean basin and to analyze the genetic structure of olive cultivar gene pools. The markers were found to have high discrimination power. On average, with a single assay it was possible to discriminate 96% of the pairwise comparisons and, with a combination of 3 loci, virtually all cultivars were distinguished. The SSR markers were also tested for their ability to assign cultivars to their geographic population of origin. A selection of 6 loci was found to maximize assignment accuracy, correctly reallocating up to 75.4% of cultivars to their population of origin. Because of the confusion surrounding the origin of most olive cultivars, their molecular identification and ascertainment of origin will be extremely useful for germplasm management and breeding.
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Affiliation(s)
- V Sarri
- Dipartimento di Biologia Cellulare e Ambientale, Sezione di Biologia Cellulare e Molecolare, Università di Perugia, Via Elce di Sotto, 06123 Perugia, Italy
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70
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Benjawan C, Chutichudet P, Chanaboon T. Effect of chemical paclobutrazol on growth, yield and quality of okra (Abelmoschus esculentus L.) Har lium cultivar in northeast Thailand. Pak J Biol Sci 2007; 10:433-438. [PMID: 19069514 DOI: 10.3923/pjbs.2007.433.438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This investigation was carried out at Mahasarakham University Experimental Farm, Mahasarakham University, Northeast Thailand in the late rainy season of the 2003 to 2004 with the use of Roi-Et soil series (Oxic Paleustults). The experiment aims to search for more information on the effect of different rates of chemical Paclobutrazol (PBZ) application on growth, yield and quality of edible okra pods. A Randomised Complete Block Design (RCDB) with four replications was used for the experiment. The experiments consisted of five treatments, i.e., 0 (T1), 4000 (T2), 8000 (T3), 12,000 (T4) and 16,000 ppm ha(-1) (T5) of chemical PBZ. The results showed that an increase in PBZ application rate highly decreased plant height, harvesting age and significantly decreased leaf area of the fifth leaf but highly increased pod length, fresh weight/pod and fresh pod yield ha(-1) of the okra plants. PBZ had no significant effect on stem diameter and diameter of pods of the okra plants. Total soluble solid, fibre content, titratable acid, vitamin C and pectin contents in pods were not affected by chemical PBZ application. Pod yield highly increased with an increase in rate of PBZ application. The highest edible pod yield reached a value of 4501 kg ha(-1) for the highest rate of PBZ application (T5).
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Affiliation(s)
- Chutichudet Benjawan
- Department of Agricultural Technology, Faculty of Technology, Mahasarakham University, Mahasarakham 44000, Thailand
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71
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Arroyo-García R, Ruiz-García L, Bolling L, Ocete R, López MA, Arnold C, Ergul A, Söylemezoğlu G, Uzun HI, Cabello F, Ibáñez J, Aradhya MK, Atanassov A, Atanassov I, Balint S, Cenis JL, Costantini L, Goris-Lavets S, Grando MS, Klein BY, McGovern PE, Merdinoglu D, Pejic I, Pelsy F, Primikirios N, Risovannaya V, Roubelakis-Angelakis KA, Snoussi H, Sotiri P, Tamhankar S, This P, Troshin L, Malpica JM, Lefort F, Martinez-Zapater JM. Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphisms. Mol Ecol 2006; 15:3707-14. [PMID: 17032268 DOI: 10.1111/j.1365-294x.2006.03049.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The domestication of the Eurasian grape (Vitis vinifera ssp. sativa) from its wild ancestor (Vitis vinifera ssp. sylvestris) has long been claimed to have occurred in Transcaucasia where its greatest genetic diversity is found and where very early archaeological evidence, including grape pips and artefacts of a 'wine culture', have been excavated. Whether from Transcaucasia or the nearby Taurus or Zagros Mountains, it is hypothesized that this wine culture spread southwards and eventually westwards around the Mediterranean basin, together with the transplantation of cultivated grape cuttings. However, the existence of morphological differentiation between cultivars from eastern and western ends of the modern distribution of the Eurasian grape suggests the existence of different genetic contribution from local sylvestris populations or multilocal selection and domestication of sylvestris genotypes. To tackle this issue, we analysed chlorotype variation and distribution in 1201 samples of sylvestris and sativa genotypes from the whole area of the species' distribution and studied their genetic relationships. The results suggest the existence of at least two important origins for the cultivated germplasm, one in the Near East and another in the western Mediterranean region, the latter of which gave rise to many of the current Western European cultivars. Indeed, over 70% of the Iberian Peninsula cultivars display chlorotypes that are only compatible with their having derived from western sylvestris populations.
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Affiliation(s)
- R Arroyo-García
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
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72
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Grassi F, Labra M, Imazio S, Rubio RO, Failla O, Scienza A, Sala F. Phylogeographical structure and conservation genetics of wild grapevine. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9118-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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73
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Barnaud A, Lacombe T, Doligez A. Linkage disequilibrium in cultivated grapevine, Vitis vinifera L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:708-16. [PMID: 16402190 DOI: 10.1007/s00122-005-0174-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Accepted: 11/30/2005] [Indexed: 05/06/2023]
Abstract
We present here the first study of linkage disequilibrium (LD) in cultivated grapevine, Vitis vinifera L. subsp. vinifera (sativa), an outcrossing highly heterozygous perennial species. Our goal was to characterize the amount and pattern of LD at the scale of a few centiMorgans (cM) between 38 microsatellite loci located on five linkage groups, in order to assess its origin and potential applications. We used a core collection of 141 cultivars representing the diversity of the cultivated compartment. LD was evaluated with both independence tests and multilocus r2, both on raw genotypic and reconstructed haplotypic data. Significant genotypic LD was found only within linkage groups, extending up to 16.8 cM. It appeared not to be influenced by the weak structure of the sample and seemed to be mainly of haplotypic origin. Significant haplotypic LD was found over 30 cM. Both genotypic and haplotypic r2 values declined to around 0.1 within 5-10 cM, suggesting a rather narrow genetic base of the cultivated compartment and limited recombination since domestication events. These first results open up a few application opportunities for association mapping of QTLs and marker assisted selection.
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Affiliation(s)
- Adeline Barnaud
- INRA, UMR DGPC Equipe Génétique Vigne, 2 place Viala, 34060, Montpellier Cedex 1, France
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74
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Snoussi H, Slimane MHB, Ruiz-García L, Martínez-Zapater JM, Arroyo-García R. Genetic relationship among cultivated and wild grapevine accessions from Tunisia. Genome 2005; 47:1211-9. [PMID: 15644980 DOI: 10.1139/g04-072] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have used nuclear and chloroplast molecular markers to genotype cultivated and wild accessions of Vitis vinifera L. from Tunisia and assess their genetic relationships. Fifty-five distinct genotypes were identified among 80 cultivated accessions, including 18 genotypic groups containing between 2 and 5 accessions per group. They could represent a total of 60 distinct cultivars owing to berry colour variation found within identical genotype groups. Most of the 55 genotypes represent unique table grape genotypes except for one of them that was found identical to the genotype of table grape cultivar Rosseti. Hybridization among cultivars as well as self pollinations seems to have played an important role in their origin since several groups of closely related cultivars were observed. Furthermore, a parentage analysis showed a high probability for a parent hybrid relationship within two groups of three cultivars. No strong genetic similarities were found between cultivated and wild samples indicating that the cultivated accessions do not derive from local Vitis vinifera L. populations but could have been introduced from other regions in historic times.
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Affiliation(s)
- H Snoussi
- Laboratory of Biotechnology, Tunisian National Agricultural Research Institute (INRAT), Rue Hédi Harry, 2049, Ariana, Tunisia
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75
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Berry DA, Wright D, Xie C, Seltzer JD, Smith JSC. Using molecular sizes of simple sequence repeats vs. discrete binned data in assessing probability of ancestry: application to maize hybrids. Genetics 2005; 170:365-74. [PMID: 15466437 PMCID: PMC1449699 DOI: 10.1534/genetics.103.022061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2003] [Accepted: 02/04/2005] [Indexed: 11/18/2022] Open
Abstract
Most inferential methods for profiling genotypes based upon the use of DNA fragments use molecular-size data transcribed into discrete bins, which are intervals of DNA fragment sizes. Categorizing into bins is labor intensive with inevitable arbitrariness that may vary between laboratories. We describe and evaluate an algorithm for determining probabilities of parentage based on raw molecular-size data without establishing bins. We determine the standard deviation of DNA fragment size and assess the association of standard deviation with fragment size. We consider a pool of potential ancestors for an index line that is a hybrid with unknown pedigree. We evaluate the identification of inbred parents of maize hybrids with simple sequence repeat data in the form of actual molecular sizes received from two laboratories. We find the standard deviation to be essentially constant over the molecular weight. We compare these results with those of parallel analyses based on these same data that had been transcribed into discrete bins by the respective laboratories. The conclusions were quite similar in the two cases, with excellent performance using either binned or molecular-size data. We demonstrate the algorithm's utility and robustness through simulations of levels of missing and misscored molecular-size data.
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Affiliation(s)
- Donald A Berry
- University of Texas M. D. Anderson Cancer Center, Houston, 77030, USA.
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76
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77
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Molina-Cano JL, Russell JR, Moralejo MA, Escacena JL, Arias G, Powell W. Chloroplast DNA microsatellite analysis supports a polyphyletic origin for barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 110:613-619. [PMID: 15723272 DOI: 10.1007/s00122-004-1878-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Accepted: 11/10/2004] [Indexed: 05/24/2023]
Abstract
Five barley chloroplast DNA microsatellites (cpSSRs) were used to study genetic relationships among a set of 186 barley accessions-34 Hordeum vulgare ssp. spontaneum (HS accessions) from Morocco, Ethiopia, Cyprus, Crete, Libya, Iraq, Iran, Turkey, Afghanistan and Israel, 122 H. vulgare ssp. vulgare landraces (HV landraces) from Spain, Bolivia (old Spanish introductions), Morocco, Libya and Ethiopia and 20 modern European spring barleys (HV cultivars). All loci were polymorphic in the material studied, with the number of alleles per locus ranging from two to three. Fifteen multi-locus haplotypes were observed, 11 in HS accessions and seven in HV landraces and cultivars. Of the seven haplotypes found in the HV lines, three were shared with the HS accessions, and four were unique. Cluster analysis revealed two main groups, one consisting of HS accessions from Ethiopia and the HV landraces from Spain, Bolivia (old Spanish), Morocco and Ethiopia, whereas the other larger group contained all of the other accessions studied. Based on these grouping and the existence of haplotypes found in the HV landraces and cultivars but not in the HS wild barley, a polyphyletic origin is proposed for barley, with further centres of origin in Ethiopia and the Western Mediterranean.
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Affiliation(s)
- J-L Molina-Cano
- Centre UdL-IRTA, Av. Rovira Roure 177, 25189, Lleida, Spain.
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